MRP_py

MRP_py parametrizes covalently modified amino acid residues for molecular dynamics simulations, generating atomistic force-field parameters and RESP-derived charges for post-translationally modified (PTM) residues.

Key Features:

• Integration with AmberTools and Gaussian: Integrates with AmberTools (requires version 15 or higher) and Gaussian to enable molecular modeling and quantum mechanical calculations.
• Charge Derivation via RESP: Derives partial charges using the Restrained Electrostatic Potential (RESP) fitting procedure.
• Force Constant Optimization: Obtains and adapts force constants by rewriting parameters from protein-specific or GAFF (General AMBER Force Field) databases.
• Interface Parameterization: Systematically parameterizes the interface between modified residues and surrounding protein residues.
• Database Compatibility: Supports parameter extraction and compatibility with a variety of protein-specific databases.

Scientific Applications:

• Molecular dynamics of modified proteins: Enables MD simulations of proteins containing covalently modified amino acid residues.
• Post-translational modification modeling: Facilitates parameterization of post-translational modifications (PTMs).
• Covalent inhibitor modeling and interface analysis: Supports parameterization for covalent binding of small-molecule inhibitors and analysis of interfacial interactions between modified residues and host proteins.

Methodology:

RESP charge derivation; adaptation and rewriting of force constants from protein-specific or GAFF databases; quantum mechanical calculations via Gaussian; integration with AmberTools (requires v15+).